Question: I used sitebuilder to create my main website but I would like to create a new and separate sitebuilder based  site into a sub folder and make it a subdomain as well.

Answer: 

Do not create a subdomain until after you have created the site builder site first.

Log into sitebuilder and click on the "New Site" button.
Uou will see your site's url in one text box and a second field to add your sub folder where you want the subdomain site to reside. Add the folder name you want to create. Do not create the folder first using File Manager or FTP. Finish creating your site and publish.
Then log into DirectAdmin control panel and add the subdomain prefix name that matches the sub folder name.

Doing it this way you can add as many sites as you want to your domain name IF your web host allows you to have multiple site builder sites per domain name. This feature is usually reserved for the PRO version of site builder and not activated in the Instant site builder version.

101sitehosting.com offers the PRO version on all plans larger than the Starter Package.